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In the present work, the problem of protein folding is addressed from the point of view of equilibrium thermodynamics. The conformation of a globular protein in solution at common temperatures is quite complicated without any geometrical symmetry, but it is an ordered state in the sense of its biological activity. This complicated conformation of a single protein molecule is destroyed upon increasing the temperature or by the addition of appropriate chemical agents, as is revealed by the loss of its activity and change of the physical properties, and so on. Once the complicated native structures having biological activity are lost, it would be natural to suppose that the native structure could hardly be restored. Nevertheless, pioneers, such as Anson and Mirsky, recognized as early as in 1925 that this was not always the case. If one defines the folded and unfolded states of a protein as two distinct phases of a system, then under the variation of temperature the system is transformed from one phase state into another and vice versa. The process of protein folding is accompanied by the release or absorption of a certain amount of energy, corresponding to the first-oder-type phase transitions in the bulk. Knowing the partition function of the system one can evaluate its energy and heat capacity under different temperatures. This task was performed in this work. The results of the developed statistical mechanics model were compared with the results of molecular dynamic simulations of alanine poylpeptides. In particular, the dependencies on temperature of the total energy of the system and heat capacity were compared for alanine polypeptides consisting of 21, 30, 40, 50 and 100 amino acids. The good correspondence of the results of the theoretical model with the results of molecular dynamics simulations allowed to validate the assumptions made about the system and to establish the accuracy range of the theory. In order to perform the comparison of the results of theoretical model and the molecular dynamics simulations it is necessary to perform the efficient analysis of the results of molecular dynamics simulations. This task was also addressed in the present work. In particular, different ways to obtain dependence of the heat capacity on temperature from molecular dynamics simulations are discussed and the most efficient one is proposed. The present thesis reports the result of molecular dynamic simulations for not only alanine polypeptides by also for valine and leucine polypeptides. In valine and leucine polypeptides, it is also possible to observe the helix↔random coil transitions with the increase of temperature. The current thesis presents a work that starts with the investigation of the fundamental degrees of freedom in polypeptides that are responsible for the conformational transitions. Then this knowledge is applied for the statistical mechanics description of helix↔coil transitions in polypeptides. Finally, the theoretical formalism is generalized for the case of proteins in water environment and the comparison of the results of the statistical mechanics model with the experimental measurements of the heat capacity on temperature dependencies for two globular proteins is performed. The presented formalism is based on fundamental physical properties of the system and provides the possibility to describe the folding↔unfolding transitions quantitatively. The combination of these two facts is the major novelty of the presented approach in comparison to the existing ones. The “transparent” physical nature of the formalism provides a possibility to further apply it to a large variety of systems and processes. For instance, it can be used for investigation of the influence of the mutations in the proteins on their stability. This task is of primary importance for design of novel proteins and drug delivering molecules in medicine. It can provide further insights into the problem of protein aggregation and formation of amyloids. The problem of protein aggregation is closely associated with various illnesses such as Alzheimer and mad cow disease. With certain modifications, the presented theoretical method can be applied to the description of the protein crystallization process, which is important for the determination of the structure of proteins with X-Rays. There many other possible applications of the ideas described in the thesis. For instance, the similar formalism can be developed for the description of melting and unzipping of DNA, growth of nanotubes, formation of fullerenes, etc.
Poster Presentation from Nineteenth Annual Computational Neuroscience Meeting: CNS*2010 San Antonio, TX, USA. 24-30 July 2010 In order to model extracellular potentials the Line-Source method provides [1] a very powerful and accurate approach. In this method transmembane fluxes are understood as sources for potential distributions which obey the Poission-equation with zero boundary conditions in the infinity. Its solutions reveal that the waveforms are proportional to local transmembrane net currents. The extracellular potentials are comparable small in amplitude and with the aid of their second special derivatives, it is possible to interpret them as additional fluxes to be included into the cable equation having an impact on the membrane potential of surrounding cells [2]. On this basis ephaptic interactions have been studied and have been considered to play a minor role in the network activity. This modeling study provides a new approach based on the first principle of the conservation of charges which leads to a generalized form of the cable equation taking into account the full three-dimensional detail of the cell’s geometry and the presence of the extracellular potential. So instead of coupling the compartment model and the model for extracellular potentials by means of the transmembrane currents, a non-linear system of partial differential equations is solved. Because the abstraction of deviding the cell’s geometry into compartments falls apart, it is possible to examine the contribution of the precise cell geometry to the signal processing while not neglecting the impact which could result from the extracellular potential. Some simulations of propagating action potentials on ramified geometries are going to be shown as well as the resulting distributions of extracellular action potentials.
Die Objekterkennung spielt für die menschliche Wahrnehmung eine zentrale Rolle. Hierzu nutzen wir das visuelle System in ähnlichem Maße wie den Tastsinn zur Exploration unserer Umwelt. In Kombination beider Sinne gelingt es uns unser Umfeld adäquat wahrzunehmen. Um postulierte Interaktionen zwischen visuellem und haptischem System aufzudecken und näher zu untersuchen, bedienten wir uns der Methode der funktionellen Magnetresonanztomographie.
Vorangehende funktionell bildgebende Studien über visuo-haptische zerebrale Informationsverarbeitung beschrieben den lateralen okzipi-talen taktil-visuellen Kortex (LOtv) und den intraparietalen Sulcus (IPS) als Hauptkandidaten für visuo-haptische Integration (Amedi et al., 2005; Sathian, 2005). Die meisten Studien betrachteten jedoch alleinig Schnittmengen aus Ergebnissen nach unimodaler Aktivierung. Um nun strengere statistische Kriterien für das Auffinden visuo-haptischer Integrationsareale zu testen (Beauchamp, 2005; Laurienti et al., 2005), suchten wir nach Regionen, welche durch direkte bimodale Stimulation stärker aktiviert werden, als nach Darbietung unimodaler Reize. Ziel dieser Arbeit war es, in Anlehnung an vorbestehende Literatur unter Zuhilfenahme strengerer statistischer Kriterien und mittels abstrakten Stimulations-Materials nach Integrationseffekten infolge simultaner visuo-haptischer Stimulation im menschlichen Gehirn zu suchen. Neurophysiologische Grundlage dieses Vorhabens ist dabei die Annahme, dass neuronale Gruppen spezifische Funktionen erfüllen und deren Aktivität über das sogenannte „Blood Oxygen Level Dependend-Signal“ (BOLD-Signal) mittels fMRT sichtbar gemacht werden kann.
Sechzehn gesunde Probanden partizipierten an der vorliegenden Studie. Während des Experiments kamen Schwarz-weiß-Fotografien und haptisch zu explorierende Figuren wahlweise von Tieren oder abstrakten Objekten zum Einsatz. Diese wurden dem jeweiligen Probanden teils als Einzelreiz (rein visuell/rein haptisch), teils simultan als visuo-haptische Reize während des fMRT-Messvorgangs dargeboten. Diese visuo-haptische Objektdarbietung führte zu einer signifikanten Aktivierung verschiedener kortikaler Gehirnregionen. Im Rahmen unseres Experiments konnten hauptsächlich drei bilaterale Regionen identifiziert werden, welche einen visuo-haptischen Integrationseffekt für das verwendete Stimulusmaterial zeigten: LOtv, IPS und das anteriore Cerebellum. Interessanterweise zeigte das rechtslaterale Cerebellum den robustesten visuo-haptischen Effekt, der weder vom Stimulusmaterial (Tiere/Fribbles), noch von der Kongruenz der dargebotenen Reize abzuhängen schien.
Aufgrund der Beobachtung, dass selbst isolierte motorische Beanspruchung Aktivationssignale im Gehirn auslösen kann, wurde ein zweites Studienprotokoll zum Ausschluss motorischer Aktivität als alleinige Komponente der Signalantwort entwickelt und eine zusätzliche rein motorische Kontrollbedingung eingeführt. Im Folgenden ließen sich die im Hauptexperiment identifizierten Regionen auch unter dieser zusätzlichen Bedingung abbilden. Mit unserem Studiendesign gelang es, die in der Literatur als multisensorisch vorbeschriebenen Regionen erneut nachzuweisen. Zusätzlich deuten unsere Ergebnisse darauf hin, dass es cerebelläre bimodal integrierende Areale gibt, welche auch in Abwesenheit zusätzlicher Aufgabenstellungen eine wichtige Rolle in visuo-haptischen Verarbeitungsprozessen spielen. Es bleibt jedoch abzuwarten, ob diese Regionen zukünftig endgültig als multisensorisch einzustufen sind.
Laut Richard Dyer haben die Menschen schon immer Serialität als Spiel mit Wiederholung und Erwartung geliebt: "It’s clear that humans have always loved seriality. Bards, jongleurs, griots and yarnspinners (not to mention parents and nurses) have all long known the value of leaving their listeners wanting more, of playing on the mix of repetition and anticipation, and indeed of the anticipation of repetition, that underpins serial pleasure. However, it is only under capitalism that seriality became a reigning principle of cultural production, starting with the serialisation of novels and cartoons, then spreading to news and movie programming." Dyer unterscheidet in seinem historischen Abriss kaum zwischen Wiederholung und Serialität. Die Menschen lieben Serialität, weil es eine Lust an der Wiederholung gibt, doch erst seit der seriellen Produktion des Kapitalismus hat sich die Serie als Format durchgesetzt. Die Wiederholung im Kinderspiel unterscheidet sich jedoch von den Fortsetzungsromanen und Fernsehserien, da hier Variation und Linearität partiell eine größere Rolle spielt, die sich nicht auf die Erwartungshaltung in der rituellen Wiederholung reduzieren lässt. Denn obwohl dem zuzustimmen ist, dass "allen serialen und seriell angebotenen Produkten [...] das stilistische Merkmal der Wiederholung gemeinsam [ist]", ist es meiner Ansicht nach notwendig, zwischen der Wiederholung und dem Seriellen in kulturellen und ästhetischen Ausdrucksformen zu unterscheiden. Daher werde ich zunächst die Wiederholung genauer skizzieren, bevor ich auf spezifische serielle Formate in Film und Fernsehen eingehe.
Vorliegende Publikation verfolgt ein anderes Konzept. Auch sie will auf interessante Angebote im digitalen Reich aufmerksam machen. Sie beschränkt sich jedoch nicht auf den bloßen Link oder den knapp kommentierten Hinweis auf ein Programm, sondern charakterisiert das jeweilige Angebot im Blick auf seine praktische Brauchbarkeit. Das Kriterium der Brauchbarkeit sind die Erfahrungen, die der Autor jeweils damit gemacht hat. Man könnte eine solche Auswahl subjektiv nennen, aber wer, außer Subjekten, kann überhaupt etwas beurteilen?
Wer gerne auf Entdeckungsreisen geht und wen immer einmal das Fernweh packt, ohne dass er Zeit und Geld für große Expeditionen hätte, für den kann Google Earth eine Art Suchtmittel darstellen. Von Ayers Rock zum Fujijama und aus den Straßenschluchten Manhattans in die afrikanische Steppe: Mit Google Earth eine Sache von Sekunden.
The first part of the following paper deals with varying points of criticism forwarded against Ordoliberalism. Here, it is not the aim to directly falsify each argument on its own; rather, the author tries to give a precise overview of the spectrum of critique. The second section picks out one argument of critical review – namely that the ordoliberal concept of the state is somewhat elitist and grounded on intellectual experts. Based on the previous sections, the final part differentiates two kinds of genesis of norms: an evolutionary and an elitist one – both (latently) present within Ordoliberalism. In combination with the two-level differentiation between individual and regulatory ethics, the essay allows for a distinction between individual-ethical norms based on an evolutionary genesis of norms and regulatory-ethical norms based on an elitist understanding of norms. A by-product of the author’s argument is a (further) demarcation within neoliberalism.
2008/9 sees the 60th anniversary of the German economic and currency reform of June 20, 1948, and the adoption of the Grundgesetz on May 23, 1949, which committed the country to the ideals of a socially committed market economy. Both of these events are important points along the path taken by the Federal Republic of Germany to reach the system of a social market economy. Since the term, Social Market Economy is often used in several different contexts and sometimes to mean contradictory things, we must ask: what exactly does the term social market economy entail? What economic-ethical ideas and theories are behind it? This paper will trace the origins of the social market economy (chapter 2) and explain the central characteristics of the Freiburg School of Economics (chapter 3), one of the main pillars of the social market economy. Central to this paper is the oeuvre of Walter Eucken, one of the leading representatives of the ordoliberal Freiburg School. The aim is to identify socio-political factors of influence and inspiration on his theory of economic policy (chapter 4) and evaluate similarities to the works of Kant, Smith and other economic philosophers. Chapter 5 will seek to elucidate Eucken’s “Program of Liberty”. We shall also allow ourselves a slight diversion to elaborate on the parallels between this work and Kant’s understanding of freedom and autonomy. Chapter 6 deals with Eucken’s dual requirements of an economic and social order (i.e. functioning and humane socio-economic order). In chapter 7, we seek to answer – with considerable reference to Adam Smith – to what extent it can be assumed that self-interest and the common good are mutually compatible. This paper concludes with a few remarks about the topicality of ordoliberalism in relation to modern, German-speaking economic ethics (chapter 8).
Sacoglossan sea slugs are unique in the animal kingdom in that they sequester and maintain active plastids that they acquire from the siphonaceous algae upon which they feed, making the animals photosynthetic. While most sacoglossan species digest their freshly ingested plastids within hours, four species from the family Plakobranchidae retain their stolen plastids (kleptoplasts) in a photosynthetically active state on time scales of weeks to months. The molecular basis of plastid maintenance within the cytosol of digestive gland cells in these photosynthetic metazoans is yet unknown, but is widely thought to involve gene transfer from the algal food source to the slugs based upon previous investigations of single genes. Indeed, normal plastid development requires hundreds of nuclear-encoded proteins, with protein turnover in photosystem II in particular known to be rapid under various conditions. Moreover, only algal plastids, not the algal nuclei, are sequestered by the animals during feeding. If algal nuclear genes are transferred to the animal either during feeding or in the germ line, and if they are expressed, then they should be readily detectable with deep-sequencing methods. We have sequenced expressed mRNAs from actively photosynthesizing, starved individuals of two photosynthetic sea slug species, Plakobranchus ocellatus Van Hasselt, 1824 and Elysia timida Risso, 1818. We find that nuclear-encoded, algal-derived genes specific to photosynthetic function are expressed neither in P. ocellatus nor in E. timida. Despite their dramatic plastid longevity, these photosynthetic sacoglossan slugs do not express genes acquired from algal nuclei in order to maintain plastid function.
Hallin and Mancini’s seminal work Comparing Media Systems: Three Models of Media and
Politics has generated great interest and enthusiasm among media scholars to advance comparative
studies by applying the four dimensions to analyze media performance in different countries. Media
scholars agree that the four variables suggested by the two authors, i.e. the structure of media
markets, political parallelism, role of the state, and professionalization of journalism, provide a
good theoretical framework for the analysis of relationship between political and media system.
Their models for comparing media systems are based on a ‘most similar’ strategy,
analysing media and journalism only in stable Western democracies (i.e. Western European and
North American nations), and the purpose of the research presented in this paper was to develop
the model to include other parts of the world as well.
The most recent attempts to integrate East Central European media systems into the Hallin
and Mancini model, the conclusion being that the East Central European media share most
similarities with the Polarized Pluralist model. This conclusion follows not only Hallin and
Mancini, but also Splichal. The researcher in his earlier works argued that the changes in post-
Soviet media systems could be best explained by referring to the concept of Italianization - the
media are under strong state control, the degree of mass media partisanship is strong, low level of
journalistic professionalism, commercialization.
In fact, out of the three models only two (the Liberal and the Democratic Corporatist
model) are models in any strict sense, whereas the third - Polarized Pluralism - is better defined
as the lack of a model: the Liberal and Democratic Corporatist model are both built on a
consensus around core values, whereas the key feature of the Polarized Pluralism model is that
there is no consensus and no core values. De Albuquerque introduced other variables that also
would be highly relevant to the comparative analysis of media systems, but that have no place in
the Hallin & Mancini framework, the most important one being whether the political system is
presidential or parliamentary. For example, it has been demonstrated that media in presidential systems are more likely to focus on individual politicians and the administrative aspects of
government, as well as acting as an intermediary between different branches of government, than
are media in parliamentary systems.
Scholars dealing with the East Central Europe (and elsewhere) are too interested in fitting
their respective nations to one of the three models, rather than focusing on the variables and on the
comparative dimension. The scholars focus on the variables and on the comparative dimension: it
is strucking that their conclusions are precisely that a strict modeling approach (i.e. trying to fit
any given nation into the three-system model) is not enough if we want to understand media
system differences properly.
Hallin and Mancini (2004: 305) write that “The Democratic Corporatist Model, we suspect,
will have particularly strong relevance for the analysis of those parts of Eastern and Central
Europe that share much of the same historical development, like Poland, Hungary, the Czech
Republic, and the Baltic States”. At the same time, however, they suspect that scholars working on
the East Central European media will find much that is relevant in their analysis of the
Mediterranean region.
The recent attempts integrate East Central European media systems into the Hallin and
Mancini model, the conclusion being that the East Central European media share most similarities
with the Polarized Pluralist model. This conclusion follows not only Hallin and Mancini, but also
Splichal. The researcher in his earlier works argued that the changes in post-Soviet media systems
could be best explaind by referring to the concept of Italianization - including the role of
clientelism, the strong role of the state, the role of the media as an instrument of political struggle,
and a low level of journalistic professionalism.
The Polarized Pluralist model all too often seems to be the default model – what is really
gained, analytically, by saying that post-Communist countries are all basically Polarized Pluralist
media system when they are different in many ways. This question needs further elaboration.
Instead of fitting the Italianization model into East Central Europe, scholars should start working on their own model, introducing other variables, that would allow them to investigate the
media in the region adequately.